R/joinGenoFulc.R

In AndersenLab/easyfulcrum: easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application

#' joinGenoFulc
#'
#' \code{joinGenoFulc} joins the collection data output from the
#' \code{procFulcrum} function with the genotyping data output from the
#' \code{checkGenotypes} function.
#'
#' @param fulc a collection data frame output from the \code{procFulcrum}
#'   function.
#' @param geno a genotyping data frame output from the \code{loadGenotypes}
#'   function.
#' @param dir OPTIONAL, the path to the project directory, if passed will
#'   save the genotyping data in data/processed/genotypes.
#' @param select_vars Logical, TRUE  will return only the default variables,
#'   FALSE will return all variables. FALSE is recommended if using customized
#'   Fulcrum applications other than "Nematode field sampling" and "Nematode
#'   isolation". FALSE is default.
#' @return A single collection dataframe with variables described in the data
#'   dictionary.
#' @import dplyr
#' @export
#'

joinGenoFulc <- function(geno, fulc, dir = NULL, select_vars = F) {
  # Save the finalized genotyping sheet if given
  if(is.character(dir)){
    saveRDS(object = geno,
         file = glue::glue("{dir}","/data/processed/genotypes/",
                           as.character(Sys.Date()),"_",
                           tail(strsplit(dir,"/")[[1]],1),"geno.rds"), version = 3)}

  # Join genotyping sheet with collection and isolation data
  out_dat <- fulc %>%
    dplyr::full_join(geno)

  # chose the selected data or not
  if(select_vars == TRUE) {
    # Reorder variables
  out_dat_selected <- out_dat %>%
    dplyr::select(project,
                  c_label,
                  s_label,
                  species_id,
                  strain_name,
                  collection_by,
                  collection_datetime_UTC,
                  collection_date_UTC,
                  collection_local_time,
                  collection_fulcrum_latitude,
                  collection_fulcrum_longitude,
                  exif_gps_latitude,
                  exif_gps_longitude,
                  collection_latitude,
                  collection_longitude,
                  collection_lat_long_method,
                  collection_lat_long_method_diff,
                  fulcrum_altitude,
                  exif_gps_altitude,
                  collection_altitude,
                  collection_altitude_method,
                  collection_location,
                  collection_island,
                  collection_trail,
                  landscape,
                  sky_view,
                  ambient_humidity,
                  substrate,
                  substrate_notes,
                  substrate_other,
                  raw_ambient_temperature,
                  proc_ambient_temperature,
                  raw_substrate_temperature,
                  proc_substrate_temperature,
                  gridsect,
                  gridsect_index,
                  gridsect_radius,
                  grid_sect_direction,
                  sample_photo1,
                  sample_photo2,
                  sample_photo3,
                  best_photo, #best_exif_dop_photo,
                  best_photo_gps_dop,
                  best_photo_caption,
                  isolation_by,
                  isolation_datetime_UTC,
                  isolation_date_UTC,
                  isolation_local_time,
                  isolation_latitude,
                  isolation_longitude,
                  isolation_photo,
                  worms_on_sample,
                  #select these variables if they exist only, avoids error if not
                  any_of(c("shipment_sent_date",
                           "shipment_received_date",
                           "proliferation_48",
                           "proliferation_168",
                           "lysis_date",
                           "general_notes",
                           "manual_blast_notes",
                            "proliferating",
                            "pcr_product_its2",
                            "pcr_product_ssu",
                            "possible_new_caeno_sp",
                            "make_strain_name",
                            "reason_strain_not_named",
                            "flag_unusual_target_species_name")),
                  flag_ambient_temperature,
                  flag_ambient_temperature_run,
                  flag_substrate_temperature,
                  flag_unusual_sample_photo_num,
                  flag_duplicated_c_label_field_sampling,
                  flag_collection_lat_long_method_diff_extreme,
                  flag_unusual_isolation_photo_num,
                  flag_duplicated_isolation_for_c_label,
                  flag_duplicated_s_label_isolation_s_labeled_plates,
                  flag_missing_s_label_isolation_s_labeled_plates,
                  flag_missing_isolation_record,
                  flag_unusual_s_label_genotyping,
                  flag_missing_s_label_genotyping,
                  flag_duplicated_s_label_genotyping)
  }
  # return data
  if(select_vars == TRUE){
    message("returning selected data, set select_vars to FALSE if variables are missing")
    return(out_dat_selected)
  }
  else{
    message("returning all data, set select_vars to TRUE if you want to select default variables")
    return(out_dat)
  }
}